I have the port in the rear deck. If it is sealed off correctly, you shouldn't get any condensation in the trunk. Speaking from experience, if you are getting condensation in the trunk, it is due to a leak in the trunk area, not from the cabin.
It is a much more effecient way to go for sound as well. It not only gives you all your bass but it also keeps your trunk in one piece, as JAYO can attest to that.... lol